Comparative Analysis of hRSV and hMPV M2-1 Structural Dynamics via Molecular Dynamics Simulations

Human Respiratory Syncytial Virus (hRSV) and Human Metapneumovirus (hMPV) are major causes of severe bronchiolitis and pneumonia, affecting infants, elderly, and immunocompromised individuals. Despite their significant global health burden, effective treatment options remain limited. A critical player in the replication cycle of both hRSV and hMPV is the M2-1 protein, a transcriptional co-factor that ensures efficient viral RNA synthesis by preventing premature dissociation of the viral polymerase complex. Structurally, M2-1 assembles into a tetrameric complex that exhibits remarkable conformational plasticity, displaying two distinct structural states: a symmetric, disk-like closed conformation (hRSV) and an asymmetric open conformation (hMPV), in which one subunit adopts a dramatically different orientation. This dynamic equilibrium between open and closed states is believed to facilitate M2-1’s dual role in binding both the viral phosphoprotein (P) and mRNA, suggesting a finely tuned regulatory mechanism governing viral transcription. To investigate the structural determinants of this conformational transition, we employed all-atom molecular dynamics simulations, combined with MM-GBSA free energy calculations. Our computational analyses revealed that a linker region (residues 53–63), which bridges the oligomerization helix and the core domain, acts as a central regulatory switch controlling the open-closed transition. Principal Component Analysis (PCA) demonstrated that mutations within this linker region induce significant alterations in protein dynamics. Free energy via MM-GBSA highlighted that specific residues within this linker contribute substantially (~ -25 kJ/mol) to the binding free energy. These findings suggest that the linker region serves as a critical hotspot for modulating M2-1’s functional dynamics. Our study also provides mechanistic insights into M2-1’s conformational equilibrium through all-atom molecular dynamics simulations of the open-state complex with adenosine monophosphate (AMP). Comparative analysis of hRSV and hMPV revealed that AMP binding exhibits greater stability in hMPV M2-1. These findings highlight how ligand interactions may modulate M2-1’s structural dynamics, with implications for targeting conformational states to disrupt viral transcription.